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- PDB-4uxz: Structure of delta7-DgkA-syn in 7.9 MAG to 2.18 angstrom resolution -
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Open data
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Basic information
Entry | Database: PDB / ID: 4uxz | ||||||
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Title | Structure of delta7-DgkA-syn in 7.9 MAG to 2.18 angstrom resolution | ||||||
![]() | DIACYLGLYCEROL KINASE-DELTA 7 | ||||||
![]() | TRANSFERASE / DIACYLGLYEROL KINASE / IN MESO CRYSTALLIZATION / LIPID CUBIC PHASE / LIPIDIC CUBIC PHASE / LIPID MESOPHASE / LIPIDIC MESOPHASE / MEMBRANE PROTEIN / MONOACYLGLYCEROL | ||||||
Function / homology | ![]() diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / response to UV / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, D. / Howe, N. / Caffrey, M. | ||||||
![]() | ![]() Title: Ternary Structure Reveals Mechanism of a Membrane Diacylglycerol Kinase. Authors: Li, D. / Stansfeld, P.J. / Sansom, M.S.P. / Keogh, A. / Vogeley, L. / Howe, N. / Lyons, J.A. / Aragao, D. / Fromme, P. / Fromme, R. / Basu, S. / Grotjohann, I. / Kupitz, C. / Rendek, K. / ...Authors: Li, D. / Stansfeld, P.J. / Sansom, M.S.P. / Keogh, A. / Vogeley, L. / Howe, N. / Lyons, J.A. / Aragao, D. / Fromme, P. / Fromme, R. / Basu, S. / Grotjohann, I. / Kupitz, C. / Rendek, K. / Weierstall, U. / Zatsepin, N.A. / Cherezov, V. / Liu, W. / Bandaru, S. / English, N.J. / Gati, C. / Barty, A. / Yefanov, O. / Chapman, H.N. / Diederichs, K. / Messerschmidt, M. / Boutet, S. / Williams, G.J. / Marvin Seibert, M. / Caffrey, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.7 KB | Display | ![]() |
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PDB format | ![]() | 114.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4uxwC ![]() 4uxxC ![]() 4uyoC ![]() 3ze3S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 14204.451 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 145 molecules ![](data/chem/img/79N.gif)
![](data/chem/img/79M.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/79M.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-79N / ( #3: Chemical | ChemComp-79M / ( #4: Chemical | ChemComp-ZN / | #5: Chemical | ChemComp-FLC / | #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE PROTEIN CONTAINS AN N-TERMINAL HIS TAG 'GHHHHHHEL'. COMPARED TO THE WILDTYPE FORM, THE PROTEIN ...THE PROTEIN CONTAINS AN N-TERMINAL HIS TAG 'GHHHHHHEL'. COMPARED TO THE WILDTYPE FORM, THE PROTEIN HAS SEVEN MUTATIONS. THEY ARE A41C, C46A, I53V, I70L, M96L, V107D AND C113A. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.04 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: lipidic cubic phase / pH: 5.6 Details: 4-6 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 0.06 M MAGNESIUM ACETATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPID CUBIC PHASE) METHOD AT 4 ...Details: 4-6 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 0.06 M MAGNESIUM ACETATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPID CUBIC PHASE) METHOD AT 4 DEGREES CELCIUS WITH THE 7.9 MONOACYLGLYCEROL (7.9 MAG) AS THE HOSTING LIPID. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2013 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03315 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→75.02 Å / Num. obs: 51820 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 42.36 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.18→2.24 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 1.7 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ZE3 Resolution: 2.18→57.965 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 24.15 / Stereochemistry target values: ML Details: THERE ARE SIX NCS-RELATED MOLECULES IN THE ASYMMETRIC UNIT BUT NCS RESTRAINTS WERE NOT USED IN THE REFINEMENT.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.18→57.965 Å
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Refine LS restraints |
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LS refinement shell |
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